python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L01_exp200917_MK919_SCD_DMSO_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L02_exp200917_MK919_SCD_CMK-01min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L03_exp200917_MK919_SCD_CMK-03min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L04_exp200917_MK919_SCD_CMK-10min_AB03.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L09_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L10_exp2011_MK846_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L11_exp2101_MK978_SCD_DMSO_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L12_exp2101_MK978_SCD_1NMPP1-01min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L13_exp2101_MK978_SCD_1NMPP1-10min_AB107.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L14_exp2101_MK999_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L15_exp2101_MK999_SCD_1NMPP1-01min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L16_exp2101_MK999_SCD_1NMPP1-03min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L17_exp2101_MK999_SCD_1NMPP1-10min_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L18_exp2101_MK554_SCGE_DMSO_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.1x36mers.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes.protein_coding.merged.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.protein_coding.merged.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-upstream500bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.TSS-250bp-350bp.bed 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes_500bp_ext 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPM -RPM -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.genes 0 2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.sacCer3.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes genes.sacCer3.2021-02-23-210117L19_exp2101_MK554_SCGE_alpha_AB101.2x36mers.unique.midPoint.RPKM -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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L01_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L02_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L03_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L04_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L05_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L06_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L07_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L08_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L09_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L10_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L11_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L12_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L13_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_AB01.2x36mers.sacCer3+C_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.2021-02-23-210128L14_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L15_exp210122_MS652c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L16_exp210122_MS656c1_SCD_EtOH-60min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L17_exp210122_MS652c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L18_exp210122_MS656c1_SCD_50-ATC-45min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L19_exp210122_MS652c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L20_exp210122_MS656c1_SCD_50-ATC-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L21_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L22_exp210122_MS652c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L23_exp210122_MS656c2_SCD_EtOH-45min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L24_exp210122_MS652c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L25_exp210122_MS656c2_SCD_50-ATC-30min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L26_exp210122_MS652c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L27_exp210122_MS656c2_SCD_50-ATC-45min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_glabrata_CBS138_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_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 2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.sacCer3+C_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.2021-02-23-210128L28_exp210122_MS205_SCD_RAPA-60min_input.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint