python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.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.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.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.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.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.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L08_MS63-sp972-30nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L09_MS422-sp109-00nM_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.2x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-upstream500bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.TSS-upstream500bp.bed 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes TSS-250bp-350bp.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes_500bp_ext.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.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 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPM -RPM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L25_MS63-MS99-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L26_MS63-MS99-30nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L31_MS212-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L32_MS212-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L33_MS213-MS99-DMSO_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L34_MS213-MS99-RAPA_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L35_MS63-MS99-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L36_MS63-MS99-30nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_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.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L41_MS212-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L42_MS212-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L43_MS213-MS99-DMSO_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L44_MS213-MS99-RAPA_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L45_MS63-MS99-00nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_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.2019-04-06-190218-L46_MS63-MS99-30nM_AB4-Rpb1CTD-S2P.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_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.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L01_MS212-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L02_MS212-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L03_MS213-MS99-DMSO_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L04_MS213-MS99-RAPA_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L05_MS63-MS99-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L06_MS63-MS99-30nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L07_MS63-sp972-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_chromosomes.nochrM.chrom.sizes genes.Candida.2019-04-06-190307-L10_MS422-sp109-00nM_input.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L11_MS212-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L12_MS212-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L13_MS213-MS99-DMSO_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L14_MS213-MS99-RAPA_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L15_MS63-MS99-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L16_MS63-MS99-30nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_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.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L21_MS212-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L22_MS212-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L23_MS213-MS99-DMSO_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/C_glabrata_CBS138_current_features.genes 0 2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_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.2019-04-06-190307-L24_MS213-MS99-RAPA_AB21-H4.1x36mers.sacCer3+C_glabrata_CBS138_current_chromosomes.unique.RPKM -excludeReadsMappingToOtherChromosomes