python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L11_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L12_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L13_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L14_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L15_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L16_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L17_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L18_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L19_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.1x36mers.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L20_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L21_exp2023-05-22-230511_MS501_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L22_exp2023-05-22-230511_MS501_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L23_exp2023-05-22-230511_MS499_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L24_exp2023-05-22-230511_MS499_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L25_exp2023-05-22-230511_MS069_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L26_exp2023-05-22-230511_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L27_exp2023-05-22-230511_MS500_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L28_exp2023-05-22-230511_MS500_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L29_exp2023-05-22-230511_MS497_SCD-MET-1hr-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.1x36mers.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230515L30_exp2023-05-22-230511_MS497_SCD-MET-4hr45min-arrest_2uMPhIAA-45min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L05_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L06_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.1x36mers.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L07_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.1x36mers.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_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.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L08_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep1.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L09_exp2023-05-22-230516_MS069_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L10_exp2023-05-22-230516_MS069_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.1x36mers.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L11_exp2023-05-22-230516_MS756_SCD-MET-1hr-arrest_2uMPhIAA-55min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.merged.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.merged.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPM -RPM -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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.1x36mers.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_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.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.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 2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida-spike-in.2023-05-22-230518L12_exp2023-05-22-230516_MS756_SCD-MET-4hr45min-arrest_2uMPhIAA-4hr-40min_DNA-rep2.2x36mers.nochrM.ERMTOC.a.midPoint.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint