python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L01_1A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L01_1A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L01_1A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L02_1B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L02_1B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L02_1B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L03_1C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L03_1C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L03_1C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L04_2A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L04_2A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L04_2A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L05_2B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L05_2B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L05_2B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L06_2C_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L06_2C_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L06_2C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L07_3A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L07_3A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L07_3A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L08_3B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L08_3B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L08_3B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L09_4A_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L09_4A_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L09_4A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L10_4B_ChIP.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200630L10_4B_ChIP.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200630L10_4B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L11_5A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L11_5A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L11_5A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L12_5B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L12_5B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L12_5B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L13_5C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L13_5C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L13_5C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L14_6A_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L14_6A_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L14_6A_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L15_6B_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L15_6B_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L15_6B_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L16_6C_ChIP.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L16_6C_ChIP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L16_6C_ChIP.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L17_MS548_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L18_MS549_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L19_MS550_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L20_MS551_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L21_MS554_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L22_MS555_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L23_MS556_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L24_MS557_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L25_MS558_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L26_MS559_SCD_37-3hr_30mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L27_MS550_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L28_MS551_SCD_37-3hr_05mfix_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L29_MS554_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe-spike-in.2020-08-27-200630L30_MS555_SCD_37-3hr_05mfix_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L01_exp200626_MK846_SCGE_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L02_exp200626_MK846_SCGE_G1_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L03_exp200626_MK846_SCGE_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L04_exp200626_MK846_SCGE_AS_RAPA_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L05_exp200704_MK846_SCD_G1_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L06_exp200704_MK846_SCD_G1_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L07_exp200704_MK846_SCD_AS_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L08_exp200704_MK846_SCD_AS_CMK_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L09_exp200625_MK846_SCD_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L10_exp200625_MK846_SCD_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L11_exp200625_MK846_SCD_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L12_exp200625_MK846_SCD_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L13_exp200625_MK846_SCD_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L14_exp200625_MK846_SCD_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L15_exp200626_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L16_exp200626_MK846_SCGE_RAPA-30m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L17_exp200626_MK846_SCGE_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L18_exp200626_MK846_SCGE_CMK-05m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L19_exp200626_MK846_SCGE_CMK-15m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L20_exp200626_MK846_SCGE_RAPA-30m_CMK-02.5m_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L21_exp2004_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200709L22_exp191120_MK846_SCGE_DMSO_AB107.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L01_exp200802_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L02_exp200802_MS208_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L03_exp200802_MS209_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L04_exp200802_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L05_exp200802_MS295_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L06_exp200802_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L07_exp200803_MS207_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L08_exp200803_MS281_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L09_exp200803_MS282_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L10_exp200803_MS294_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L11_exp200803_MS299_RAPA40_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L12_exp200803_MS289_RAPA65_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L13_exp200802_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L14_exp200802_MS208_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L15_exp200802_MS209_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L16_exp200802_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L17_exp200802_MS295_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L18_exp200802_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L19_exp200803_MS207_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L20_exp200803_MS281_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L21_exp200803_MS282_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L22_exp200803_MS294_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L23_exp200803_MS299_RAPA40_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L24_exp200803_MS289_RAPA65_AB01.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L25_MS689_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes.protein_coding.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.protein_coding.merged.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes.merged.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.merged.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-250bp-350bp.bed 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes_500bp_ext 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2020-08-27-200808L26_MS711_SCE_AB101.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint