python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPM -RPM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s31-7-190811_L01_MS398_input/2018-10-14-s31-7-190811_L01_MS398_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s31-7-190811_L01_MS398_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s32-7-190811_L02_MS398_AB102/2018-10-14-s32-7-190811_L02_MS398_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s32-7-190811_L02_MS398_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s33-7-190811_L03_MS398_AB103/2018-10-14-s33-7-190811_L03_MS398_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s33-7-190811_L03_MS398_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s34-8-190811_L04_MS399_input/2018-10-14-s34-8-190811_L04_MS399_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s34-8-190811_L04_MS399_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s35-8-190811_L05_MS399_AB103/2018-10-14-s35-8-190811_L05_MS399_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s35-8-190811_L05_MS399_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s36-8-180911_L06_MS399_AB103_PC/2018-10-14-s36-8-180911_L06_MS399_AB103_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s36-8-180911_L06_MS399_AB103_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s37-9-180911_L07_MS401_input/2018-10-14-s37-9-180911_L07_MS401_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s37-9-180911_L07_MS401_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s38-9-180911_L08_MS401_AB102/2018-10-14-s38-9-180911_L08_MS401_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s38-9-180911_L08_MS401_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s39-9-180911_L09_MS401_AB103/2018-10-14-s39-9-180911_L09_MS401_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s39-9-180911_L09_MS401_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s40-10-180911_L10_MS409_input/2018-10-14-s40-10-180911_L10_MS409_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s40-10-180911_L10_MS409_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s41-10-180911_L11_MS409_AB102/2018-10-14-s41-10-180911_L11_MS409_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s41-10-180911_L11_MS409_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5/2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s4-1-180917_L04_MS230_DMSO_AB5.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s42-10-180911_L12_MS409_AB102_PC/2018-10-14-s42-10-180911_L12_MS409_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s42-10-180911_L12_MS409_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s43-11-180911_L13_MS402_input/2018-10-14-s43-11-180911_L13_MS402_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s43-11-180911_L13_MS402_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s44-11-180911_L14_MS402_AB102/2018-10-14-s44-11-180911_L14_MS402_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s44-11-180911_L14_MS402_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s45-11-180911_L15_MS402_AB102_PC/2018-10-14-s45-11-180911_L15_MS402_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s45-11-180911_L15_MS402_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s46-12-180911_L16_MS410_input/2018-10-14-s46-12-180911_L16_MS410_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s46-12-180911_L16_MS410_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s47-12-180911_L17_MS410_AB102/2018-10-14-s47-12-180911_L17_MS410_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s47-12-180911_L17_MS410_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s48-12-180911_L18_MS410_AB102_PC/2018-10-14-s48-12-180911_L18_MS410_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s48-12-180911_L18_MS410_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s49-13-180911_L19_MS403_input/2018-10-14-s49-13-180911_L19_MS403_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s49-13-180911_L19_MS403_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s50-13-180911_L20_MS403_AB102/2018-10-14-s50-13-180911_L20_MS403_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s50-13-180911_L20_MS403_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s51-13-180911_L21_MS403_AB102_B/2018-10-14-s51-13-180911_L21_MS403_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s51-13-180911_L21_MS403_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20/2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s5-1-180917_L05_MS230_DMSO_AB20.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s52-14-180911_L22_MS411_input/2018-10-14-s52-14-180911_L22_MS411_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s52-14-180911_L22_MS411_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s53-14-180911_L23_MS411_AB102/2018-10-14-s53-14-180911_L23_MS411_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s53-14-180911_L23_MS411_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s54-14-180911_L24_MS411_AB102_B/2018-10-14-s54-14-180911_L24_MS411_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s54-14-180911_L24_MS411_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s55-15-180911_L25_MS404_input/2018-10-14-s55-15-180911_L25_MS404_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s55-15-180911_L25_MS404_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s56-15-180911_L26_MS404_AB103/2018-10-14-s56-15-180911_L26_MS404_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s56-15-180911_L26_MS404_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s57-15-180911_L27_MS404_AB103_B/2018-10-14-s57-15-180911_L27_MS404_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s57-15-180911_L27_MS404_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s58-16-180911_L28_MS412_input/2018-10-14-s58-16-180911_L28_MS412_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s58-16-180911_L28_MS412_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s59-16-180911_L29_MS412_AB102/2018-10-14-s59-16-180911_L29_MS412_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s59-16-180911_L29_MS412_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s60-16-180911_L30_MS412_AB102_B/2018-10-14-s60-16-180911_L30_MS412_AB102_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s60-16-180911_L30_MS412_AB102_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s61-17-180911_L31_MS405_input/2018-10-14-s61-17-180911_L31_MS405_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s61-17-180911_L31_MS405_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s62-17-180911_L32_MS405_AB102/2018-10-14-s62-17-180911_L32_MS405_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s62-17-180911_L32_MS405_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s6-2-180917_L6_MS231_DMSO_input/2018-10-14-s6-2-180917_L6_MS231_DMSO_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s6-2-180917_L6_MS231_DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s63-17-180911_L33_MS405_AB102_PC/2018-10-14-s63-17-180911_L33_MS405_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s63-17-180911_L33_MS405_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s64-18-180911_L34_MS413_input/2018-10-14-s64-18-180911_L34_MS413_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s64-18-180911_L34_MS413_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s65-18-180911_L35_MS413_AB102/2018-10-14-s65-18-180911_L35_MS413_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s65-18-180911_L35_MS413_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s66-18-180911_L36_MS413_AB102_PC/2018-10-14-s66-18-180911_L36_MS413_AB102_PC.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s66-18-180911_L36_MS413_AB102_PC.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s67-19-180911_L37_MS406_input/2018-10-14-s67-19-180911_L37_MS406_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s67-19-180911_L37_MS406_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s68-19-180911_L38_MS406_AB103/2018-10-14-s68-19-180911_L38_MS406_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s68-19-180911_L38_MS406_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s69-19-180911_L39_MS406_AB103_B/2018-10-14-s69-19-180911_L39_MS406_AB103_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s69-19-180911_L39_MS406_AB103_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s70-20-180911_L40_MS414_input/2018-10-14-s70-20-180911_L40_MS414_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s70-20-180911_L40_MS414_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s71-20-180911_L41_MS414_AB102/2018-10-14-s71-20-180911_L41_MS414_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s71-20-180911_L41_MS414_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1/2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s7-2-180917_L7_MS231_DMSO_AB1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s72-21-180911_L43_MS407_input/2018-10-14-s72-21-180911_L43_MS407_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s72-21-180911_L43_MS407_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s73-21-180911_L44_MS407_AB103/2018-10-14-s73-21-180911_L44_MS407_AB103.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s73-21-180911_L44_MS407_AB103.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s74-22-180911_L46_MS415_input/2018-10-14-s74-22-180911_L46_MS415_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s74-22-180911_L46_MS415_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-10-14-s75-22-180911_L47_MS415_AB102/2018-10-14-s75-22-180911_L47_MS415_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-10-14-s75-22-180911_L47_MS415_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L01_MS1-sp101_input/2018-11-08-180926_L01_MS1-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L01_MS1-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L02_MS1-sp101_AB104/2018-11-08-180926_L02_MS1-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L02_MS1-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L03_MS1-sp101_AB105/2018-11-08-180926_L03_MS1-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L03_MS1-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L04_MS398-sp101_input/2018-11-08-180926_L04_MS398-sp101_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L04_MS398-sp101_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L05_MS398-sp101_AB104/2018-11-08-180926_L05_MS398-sp101_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L05_MS398-sp101_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L06_MS398-sp101_AB105/2018-11-08-180926_L06_MS398-sp101_AB105.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L06_MS398-sp101_AB105.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L07_MS1-sp108_input/2018-11-08-180926_L07_MS1-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L07_MS1-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L08_MS1-sp108_AB102/2018-11-08-180926_L08_MS1-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L08_MS1-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L09_MS407-sp108_input/2018-11-08-180926_L09_MS407-sp108_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L09_MS407-sp108_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L10_MS407-sp108_AB102/2018-11-08-180926_L10_MS407-sp108_AB102.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L10_MS407-sp108_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L11_MS407-sp108_AB104/2018-11-08-180926_L11_MS407-sp108_AB104.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L11_MS407-sp108_AB104.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L12_MS1-sp109_input/2018-11-08-180926_L12_MS1-sp109_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L12_MS1-sp109_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L13_MS421-sp109_AB107/2018-11-08-180926_L13_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L13_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L14_MS421-sp109_AB108/2018-11-08-180926_L14_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L14_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L15_MS421-sp109_F_input/2018-11-08-180926_L15_MS421-sp109_F_input.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L15_MS421-sp109_F_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L16_MS421-sp109_AB107/2018-11-08-180926_L16_MS421-sp109_AB107.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L16_MS421-sp109_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L17_MS421-sp109_AB107.2/2018-11-08-180926_L17_MS421-sp109_AB107.2.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L17_MS421-sp109_AB107.2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L18_MS421-sp109_AB108/2018-11-08-180926_L18_MS421-sp109_AB108.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L18_MS421-sp109_AB108.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L19_MS421-sp109_AB01/2018-11-08-180926_L19_MS421-sp109_AB01.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L19_MS421-sp109_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2018-11-08-180926_L20_MS421-sp109_AB04/2018-11-08-180926_L20_MS421-sp109_AB04.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2018-11-08-180926_L20_MS421-sp109_AB04.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L01-S18_B/2019-01-03-181030L01-S18_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L01-S18_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L02-S19_B/2019-01-03-181030L02-S19_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L02-S19_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L03-S20_B/2019-01-03-181030L03-S20_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L03-S20_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L04-S21_B/2019-01-03-181030L04-S21_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L04-S21_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L05-S22_B/2019-01-03-181030L05-S22_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L05-S22_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L06-S23_B/2019-01-03-181030L06-S23_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L06-S23_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L07-S24_B/2019-01-03-181030L07-S24_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L07-S24_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L08-S25_B/2019-01-03-181030L08-S25_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L08-S25_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L09-S26_B/2019-01-03-181030L09-S26_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L09-S26_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L10-S27_B/2019-01-03-181030L10-S27_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L10-S27_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L11-S28_B/2019-01-03-181030L11-S28_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L11-S28_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L12-S29_B/2019-01-03-181030L12-S29_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L12-S29_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L13-S30_B/2019-01-03-181030L13-S30_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L13-S30_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L14-S31_B/2019-01-03-181030L14-S31_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L14-S31_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L15-S32_B/2019-01-03-181030L15-S32_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L15-S32_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L16-S33_B/2019-01-03-181030L16-S33_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L16-S33_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L17-S34_B/2019-01-03-181030L17-S34_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L17-S34_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L18-S35_B/2019-01-03-181030L18-S35_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L18-S35_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181030L19-S36_B/2019-01-03-181030L19-S36_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181030L19-S36_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B/2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L01_MS405_sp114_mix1_input-S01_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B/2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L02_MS405_sp114_mix2_input-S02_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B/2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L03_MS407_sp116_mix1_input-S03_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B/2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L04_MS407_sp116_mix2_input-S04_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L05_MS1_sp108_input-S05_B/2019-01-03-181126L05_MS1_sp108_input-S05_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L05_MS1_sp108_input-S05_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L06_MS407_sp108_input-S06_B/2019-01-03-181126L06_MS407_sp108_input-S06_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L06_MS407_sp108_input-S06_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B/2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L07_MS405_sp114_mix1_ab102A-S07_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B/2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L08_MS405_sp114_mix1_ab102B-S08_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B/2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L09_MS405_sp114_mix2_ab102A-S09_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B/2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L10_MS405_sp114_mix2_ab102B-S10_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B/2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L11_MS407_sp116_mix1_ab102A-S11_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B/2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L12_MS407_sp116_mix1_ab102B-S12_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B/2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L13_MS407_sp116_mix2_ab102A-S13_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B/2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L14_MS407_sp116_mix2_ab102B-S14_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B/2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L15_MS1_sp108_ab102B-S15_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B/2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L16_MS407_sp108_ab102A-S16_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B/2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.sacCer3+Schizosaccharomyces_pombe.a.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-01-03-181126L17_MS407_sp108_ab102B-S17_B.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L01_MS1_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L02_MS438_0nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L03_MS438_10nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L04_MS438_30nM_sp124_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L05_MS1_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L09_MS1_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L13_MS1_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L14_MS441_0nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L15_MS441_10nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L16_MS441_30nM_sp127_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L21_MS1_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L01_MS1_sp111_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L02_MS432_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L03_MS432_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L04_MS432_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L05_MS1_sp115_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L06_MS436_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L07_MS436_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L08_MS436_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L09_MS1A_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L10_MS430_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L11_MS430_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L12_MS430_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L13_MS1B_sp112_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L14_MS433_0nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L15_MS433_10nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L16_MS433_30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L17_MS1_sp111_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L18_MS432_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L19_MS432_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L20_MS432_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L21_MS1_sp115_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L22_MS436_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L23_MS436_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L24_MS436_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L25_MS1A_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L26_MS430_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L27_MS430_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L28_MS430_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L29_MS1B_sp112_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L30_MS433_0nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L31_MS433_10nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L32_MS433_30nM_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L33_MS1_sp111_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L34_MS432_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L35_MS432_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L36_MS432_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L37_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L38_MS436_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L39_MS436_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L40_MS436_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L41_MS1A_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L42_MS430_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L43_MS430_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L44_MS430_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L45_MS1B_sp112_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L46_MS433_0nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L47_MS433_10nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L48_MS433_30nM_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-02-15-190121_L49_MS1_sp115_AB102.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L01_MS430_0nM-sp110-input/2019-03-13-190218L01_MS430_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L01_MS430_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L02_MS430_10nM-sp110-input/2019-03-13-190218L02_MS430_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L02_MS430_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L03_MS430_30nM-sp110-input/2019-03-13-190218L03_MS430_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L03_MS430_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L04_MS431_0nM-sp110-input/2019-03-13-190218L04_MS431_0nM-sp110-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.protein_coding.merged.2019-03-13-190218L04_MS431_0nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L05_MS431_10nM-sp110-input/2019-03-13-190218L05_MS431_10nM-sp110-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.protein_coding.merged.2019-03-13-190218L05_MS431_10nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L06_MS431_30nM-sp110-input/2019-03-13-190218L06_MS431_30nM-sp110-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.protein_coding.merged.2019-03-13-190218L06_MS431_30nM-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L07_MS1-sp110-input/2019-03-13-190218L07_MS1-sp110-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.protein_coding.merged.2019-03-13-190218L07_MS1-sp110-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L08_MS434_0nM-sp113-input/2019-03-13-190218L08_MS434_0nM-sp113-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.protein_coding.merged.2019-03-13-190218L08_MS434_0nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L09_MS434_10nM-sp113-input/2019-03-13-190218L09_MS434_10nM-sp113-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.protein_coding.merged.2019-03-13-190218L09_MS434_10nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L10_MS434_30nM-sp113-input/2019-03-13-190218L10_MS434_30nM-sp113-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.protein_coding.merged.2019-03-13-190218L10_MS434_30nM-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L11_MS1-sp113-input/2019-03-13-190218L11_MS1-sp113-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.protein_coding.merged.2019-03-13-190218L11_MS1-sp113-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L12_MS1-sp112-input/2019-03-13-190218L12_MS1-sp112-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.protein_coding.merged.2019-03-13-190218L12_MS1-sp112-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L13_MS435_0nM-sp114-input/2019-03-13-190218L13_MS435_0nM-sp114-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.protein_coding.merged.2019-03-13-190218L13_MS435_0nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L14_MS435_10nM-sp114-input/2019-03-13-190218L14_MS435_10nM-sp114-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.protein_coding.merged.2019-03-13-190218L14_MS435_10nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L15_MS435_30nM-sp114-input/2019-03-13-190218L15_MS435_30nM-sp114-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.protein_coding.merged.2019-03-13-190218L15_MS435_30nM-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L16_MS1-sp114-input/2019-03-13-190218L16_MS1-sp114-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.protein_coding.merged.2019-03-13-190218L16_MS1-sp114-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L17_MS437_0nM-sp116-input/2019-03-13-190218L17_MS437_0nM-sp116-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.protein_coding.merged.2019-03-13-190218L17_MS437_0nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L18_MS437_10nM-sp116-input/2019-03-13-190218L18_MS437_10nM-sp116-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.protein_coding.merged.2019-03-13-190218L18_MS437_10nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L19_MS437_30nM-sp116-input/2019-03-13-190218L19_MS437_30nM-sp116-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.protein_coding.merged.2019-03-13-190218L19_MS437_30nM-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L20_MS1-sp116-input/2019-03-13-190218L20_MS1-sp116-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.protein_coding.merged.2019-03-13-190218L20_MS1-sp116-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L21_MS437B_0nM-sp115-input/2019-03-13-190218L21_MS437B_0nM-sp115-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.protein_coding.merged.2019-03-13-190218L21_MS437B_0nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L22_MS437B_10nM-sp115-input/2019-03-13-190218L22_MS437B_10nM-sp115-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.protein_coding.merged.2019-03-13-190218L22_MS437B_10nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L23_MS437B_30nM-sp115-input/2019-03-13-190218L23_MS437B_30nM-sp115-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.protein_coding.merged.2019-03-13-190218L23_MS437B_30nM-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L24_MS1-sp115-input/2019-03-13-190218L24_MS1-sp115-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.protein_coding.merged.2019-03-13-190218L24_MS1-sp115-input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP/2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L25_MS430_0nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP/2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L26_MS430_10nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP/2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L27_MS430_30nM-sp110-AB101-TBP.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2/2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L28_MS431_0nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2/2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L29_MS431_10nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2/2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L30_MS431_30nM-sp110-AB101-TOA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L31_MS1-sp110-AB101/2019-03-13-190218L31_MS1-sp110-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L31_MS1-sp110-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2/2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L32_MS434_0nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2/2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L33_MS434_10nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2/2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L34_MS434_30nM-sp113-AB101-TFA2.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L35_MS1-sp113-AB101/2019-03-13-190218L35_MS1-sp113-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L35_MS1-sp113-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L36_MS1-sp112_A-AB101/2019-03-13-190218L36_MS1-sp112_A-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L36_MS1-sp112_A-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L37_MS1-sp112_B-AB101/2019-03-13-190218L37_MS1-sp112_B-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L37_MS1-sp112_B-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1/2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L38_MS435_0nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1/2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L39_MS435_10nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L40_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L41_MS1-sp114-AB101/2019-03-13-190218L41_MS1-sp114-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L41_MS1-sp114-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28/2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L42_MS437_0nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28/2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L43_MS437_10nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28/2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L44_MS437_30nM-sp116-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L45_MS1-sp116-AB101/2019-03-13-190218L45_MS1-sp116-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L45_MS1-sp116-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28/2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L46_MS437B_0nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L47_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28/2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L48_MS437B_30nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L49_MS1-sp115-AB101/2019-03-13-190218L49_MS1-sp115-AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L49_MS1-sp115-AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1/2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L50_MS430_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1/2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L51_MS430_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1/2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L52_MS430_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1/2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L53_MS431_0nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1/2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L54_MS431_10nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1/2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L55_MS431_30nM-sp110-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L56_MS1-sp110-AB107/2019-03-13-190218L56_MS1-sp110-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L56_MS1-sp110-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1/2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L57_MS434_0nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1/2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L58_MS434_10nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1/2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L59_MS434_30nM-sp113-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L60_MS1-sp113-AB107/2019-03-13-190218L60_MS1-sp113-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L60_MS1-sp113-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L61_MS1-sp112_A-AB107/2019-03-13-190218L61_MS1-sp112_A-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L61_MS1-sp112_A-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L62_MS1-sp112_B-AB107/2019-03-13-190218L62_MS1-sp112_B-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L62_MS1-sp112_B-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1/2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L63_MS435_0nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1/2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L64_MS435_10nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1/2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L65_MS435_30nM-sp114-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L66_MSMS1-sp114-AB107/2019-03-13-190218L66_MSMS1-sp114-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L66_MSMS1-sp114-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1/2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L67_MS437_0nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1/2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L68_MS437_10nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1/2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L69_MS437_30nM-sp116-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L70_MS1-sp116-AB107/2019-03-13-190218L70_MS1-sp116-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L70_MS1-sp116-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1/2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L71_MS437B_0nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1/2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L72_MS437B_10nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1/2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L73_MS437B_30nM-sp115-AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L74_MS1-sp115-AB107/2019-03-13-190218L74_MS1-sp115-AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L74_MS1-sp115-AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1/2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L75_MS435_30nM-sp114-AB101-TFG1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28/2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-03-13-190218L76_MS437B_10nM-sp115-AB101-KIN28.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L27_MS63-sp972-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4/2019-04-06-190218-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.protein_coding.merged.2019-04-06-190218-L28_MS63-sp972-30nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L29_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L29_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4/2019-04-06-190218-L30_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L30_MS422-sp109-00nM_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L37_MS63-sp972-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD/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.protein_coding.merged.2019-04-06-190218-L38_MS63-sp972-30nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L39_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L39_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD/2019-04-06-190218-L40_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190218-L40_MS422-sp109-00nM_AB1-Rpb1CTD.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L47_MS63-sp972-00nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P/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.protein_coding.merged.2019-04-06-190218-L48_MS63-sp972-30nM_AB4-Rpb1CTD-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-04-06-190218-L49_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG/2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-04-06-190218-L50_MS422-sp109-00nM_AB107-Rpb1-FLAG.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L07_MS63-sp972-00nM_input/2019-04-06-190307-L07_MS63-sp972-00nM_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.protein_coding.merged.2019-04-06-190307-L07_MS63-sp972-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L08_MS63-sp972-30nM_input/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.protein_coding.merged.2019-04-06-190307-L08_MS63-sp972-30nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L09_MS422-sp109-00nM_input/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.protein_coding.merged.2019-04-06-190307-L09_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L10_MS422-sp109-00nM_input/2019-04-06-190307-L10_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.protein_coding.merged.2019-04-06-190307-L10_MS422-sp109-00nM_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L17_MS63-sp972-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3/2019-04-06-190307-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.protein_coding.merged.2019-04-06-190307-L18_MS63-sp972-30nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L19_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L19_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3/2019-04-06-190307-L20_MS422-sp109-00nM_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.protein_coding.merged.2019-04-06-190307-L20_MS422-sp109-00nM_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L19_207-RAPA_input/2019-08-28-MS190807L19_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L19_207-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L20_249-RAPA_input/2019-08-28-MS190807L20_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L20_249-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L21_250-RAPA_input/2019-08-28-MS190807L21_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L21_250-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L22_297-RAPA_input/2019-08-28-MS190807L22_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L22_297-RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L23_250-DMSO_input/2019-08-28-MS190807L23_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L23_250-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L24_297-DMSO_input/2019-08-28-MS190807L24_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L24_297-DMSO_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L25_207-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L26_249-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L27_250-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag/2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L28_297-RAPA_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L29_250-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag/2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L30_297-DMSO_AB107-Rpb1-Flag.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L31_207-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L32_249-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L33_250-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P/2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L34_297-RAPA_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L35_250-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P/2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-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.protein_coding.merged.2019-08-28-MS190807L36_297-DMSO_AB4-Rpb1-S2P.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L37_207-RAPA_AB20-H3/2019-08-28-MS190807L37_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L37_207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L38_249-RAPA_AB20-H3/2019-08-28-MS190807L38_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L38_249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L39_250-RAPA_AB20-H3/2019-08-28-MS190807L39_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L39_250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L40_297-RAPA_AB20-H3/2019-08-28-MS190807L40_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L40_297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L41_250-DMSO_AB20-H3/2019-08-28-MS190807L41_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L41_250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L42_297-DMSO_AB20-H3/2019-08-28-MS190807L42_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L42_297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L43_207-RAPA_AB21-H4/2019-08-28-MS190807L43_207-RAPA_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.protein_coding.merged.2019-08-28-MS190807L43_207-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L44_249-RAPA_AB21-H4/2019-08-28-MS190807L44_249-RAPA_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.protein_coding.merged.2019-08-28-MS190807L44_249-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L45_250-RAPA_AB21-H4/2019-08-28-MS190807L45_250-RAPA_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.protein_coding.merged.2019-08-28-MS190807L45_250-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L46_297-RAPA_AB21-H4/2019-08-28-MS190807L46_297-RAPA_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.protein_coding.merged.2019-08-28-MS190807L46_297-RAPA_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L47_250-DMSO_AB21-H4/2019-08-28-MS190807L47_250-DMSO_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.protein_coding.merged.2019-08-28-MS190807L47_250-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L48_297-DMSO_AB21-H4/2019-08-28-MS190807L48_297-DMSO_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.protein_coding.merged.2019-08-28-MS190807L48_297-DMSO_AB21-H4.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-08-28-MS190807L49_250-DMSO_input_R/2019-08-28-MS190807L49_250-DMSO_input_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-08-28-MS190807L49_250-DMSO_input_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1/2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L43_MS207-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1/2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L44_MS249-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1/2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L45_MS250-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1/2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L46_MS297-RAPA_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1/2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L47_MS250-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1/2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L48_MS297-DMSO_AB107-Rpb1.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L49_MS207-RAPA_AB20-H3/2019-10-07-190923L49_MS207-RAPA_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.protein_coding.merged.2019-10-07-190923L49_MS207-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L50_MS249-RAPA_AB20-H3/2019-10-07-190923L50_MS249-RAPA_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.protein_coding.merged.2019-10-07-190923L50_MS249-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L51_MS250-RAPA_AB20-H3/2019-10-07-190923L51_MS250-RAPA_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.protein_coding.merged.2019-10-07-190923L51_MS250-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L52_MS297-RAPA_AB20-H3/2019-10-07-190923L52_MS297-RAPA_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.protein_coding.merged.2019-10-07-190923L52_MS297-RAPA_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L53_MS250-DMSO_AB20-H3/2019-10-07-190923L53_MS250-DMSO_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.protein_coding.merged.2019-10-07-190923L53_MS250-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L54_MS297-DMSO_AB20-H3/2019-10-07-190923L54_MS297-DMSO_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.protein_coding.merged.2019-10-07-190923L54_MS297-DMSO_AB20-H3.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R/2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L79_MS207-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R/2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L80_MS249-RAPA_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R/2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L81_MS297-DMSO_AB107-Rpb1_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R/2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-10-07-190923L82_MS207-RAPA_AB20-H3_R.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107/2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L01_MS534_GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107/2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L02_MS535_LacI-GFP-NLS-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107/2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L03_MS536c1_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107/2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L04_MS536c2_3xFLAG-WHI5_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L05_MS537c1_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107/2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L06_MS537c2_3xFLAG-WHI5_WIQ_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107/2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L07_MS538c1_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107/2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L08_MS538c2_WHI5-5xFLAG_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107/2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L09_JK01_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107/2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L10_JK05_EMM4S-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107/2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L11_JK01_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107/2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2019-12-03-191113L12_JK05_EMM-IL-MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L01_MS1_AB107/2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L01_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L02_MS550_AB107/2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L02_MS550_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L03_MS551_FrA_AB107/2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L03_MS551_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L04_MS551_FrB_AB107/2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L04_MS551_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L05_MS551_FrC_AB107/2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L05_MS551_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L06_MS1_AB107/2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L06_MS1_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L07_MS554_AB107/2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L07_MS554_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L08_MS555_FrA_AB107/2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L08_MS555_FrA_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L09_MS555_FrB_AB107/2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L09_MS555_FrB_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L10_MS555_FrC_AB107/2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-191218L10_MS555_FrC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L11_MS1_input/2020-02-21-191218L11_MS1_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.protein_coding.merged.2020-02-21-191218L11_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L12_MS550_input/2020-02-21-191218L12_MS550_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.protein_coding.merged.2020-02-21-191218L12_MS550_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L13_MS551_FrA_input/2020-02-21-191218L13_MS551_FrA_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.protein_coding.merged.2020-02-21-191218L13_MS551_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L14_MS551_FrB_input/2020-02-21-191218L14_MS551_FrB_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.protein_coding.merged.2020-02-21-191218L14_MS551_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L15_MS551_FrC_input/2020-02-21-191218L15_MS551_FrC_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.protein_coding.merged.2020-02-21-191218L15_MS551_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L16_MS1_input/2020-02-21-191218L16_MS1_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.protein_coding.merged.2020-02-21-191218L16_MS1_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L17_MS554_input/2020-02-21-191218L17_MS554_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.protein_coding.merged.2020-02-21-191218L17_MS554_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L18_MS555_FrA_input/2020-02-21-191218L18_MS555_FrA_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.protein_coding.merged.2020-02-21-191218L18_MS555_FrA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L19_MS555_FrB_input/2020-02-21-191218L19_MS555_FrB_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.protein_coding.merged.2020-02-21-191218L19_MS555_FrB_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-191218L20_MS555_FrC_input/2020-02-21-191218L20_MS555_FrC_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.protein_coding.merged.2020-02-21-191218L20_MS555_FrC_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L19_MS207_RAPA100_input/2020-02-21-200201L19_MS207_RAPA100_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.protein_coding.merged.2020-02-21-200201L19_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L20_MS249_RAPA100_input/2020-02-21-200201L20_MS249_RAPA100_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.protein_coding.merged.2020-02-21-200201L20_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L21_MS250_RAPA100_input/2020-02-21-200201L21_MS250_RAPA100_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.protein_coding.merged.2020-02-21-200201L21_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L22_MS297_RAPA040_input/2020-02-21-200201L22_MS297_RAPA040_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.protein_coding.merged.2020-02-21-200201L22_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L23_MS297_RAPA100_input/2020-02-21-200201L23_MS297_RAPA100_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.protein_coding.merged.2020-02-21-200201L23_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L24_MS297_RAPAON_input/2020-02-21-200201L24_MS297_RAPAON_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.protein_coding.merged.2020-02-21-200201L24_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L43_MS207_RAPA100_AB01/2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L43_MS207_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L44_MS249_RAPA100_AB01/2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L44_MS249_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L45_MS250_RAPA100_AB01/2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L45_MS250_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L46_MS297_RAPA040_AB01/2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L46_MS297_RAPA040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L47_MS297_RAPA100_AB01/2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L47_MS297_RAPA100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-02-21-200201L48_MS297_RAPAON_AB01/2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-02-21-200201L48_MS297_RAPAON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L19_MS207_RAPA_input/2020-03-16-200216L19_MS207_RAPA_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.protein_coding.merged.2020-03-16-200216L19_MS207_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L20_MS249_RAPA_input/2020-03-16-200216L20_MS249_RAPA_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.protein_coding.merged.2020-03-16-200216L20_MS249_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L21_MS50_RAPA_input/2020-03-16-200216L21_MS50_RAPA_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.protein_coding.merged.2020-03-16-200216L21_MS50_RAPA_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L22_MS297_RAPA-040_input/2020-03-16-200216L22_MS297_RAPA-040_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.protein_coding.merged.2020-03-16-200216L22_MS297_RAPA-040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L23_MS297_RAPA-100_input/2020-03-16-200216L23_MS297_RAPA-100_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.protein_coding.merged.2020-03-16-200216L23_MS297_RAPA-100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L24_MS297_RAPA-ON_input/2020-03-16-200216L24_MS297_RAPA-ON_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.protein_coding.merged.2020-03-16-200216L24_MS297_RAPA-ON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L43_MS207_RAPA_AB01/2020-03-16-200216L43_MS207_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L43_MS207_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L44_MS249_RAPA_AB01/2020-03-16-200216L44_MS249_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L44_MS249_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L45_MS50_RAPA_AB01/2020-03-16-200216L45_MS50_RAPA_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L45_MS50_RAPA_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L46_MS297_RAPA-040_AB01/2020-03-16-200216L46_MS297_RAPA-040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L46_MS297_RAPA-040_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L47_MS297_RAPA-100_AB01/2020-03-16-200216L47_MS297_RAPA-100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L47_MS297_RAPA-100_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200216L48_MS297_RAPA-ON_AB01/2020-03-16-200216L48_MS297_RAPA-ON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200216L48_MS297_RAPA-ON_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L49_MS521_SCE_AB101/2020-03-16-200218L49_MS521_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L49_MS521_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L50_MS522_SCE_AB101/2020-03-16-200218L50_MS522_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L50_MS522_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L51_MS523_SCE_AB101/2020-03-16-200218L51_MS523_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L51_MS523_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L52_MS524_SCE_AB101/2020-03-16-200218L52_MS524_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L52_MS524_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L53_MS528_SCE_AB101/2020-03-16-200218L53_MS528_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L53_MS528_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L54_MS529_SCE_AB101/2020-03-16-200218L54_MS529_SCE_AB101.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L54_MS529_SCE_AB101.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L55_MK846_DD_AB01/2020-03-16-200218L55_MK846_DD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L55_MK846_DD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L56_MK846_DC_AB01/2020-03-16-200218L56_MK846_DC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L56_MK846_DC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L57_MK846_RD_AB01/2020-03-16-200218L57_MK846_RD_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L57_MK846_RD_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L58_MK846_RC_AB01/2020-03-16-200218L58_MK846_RC_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L58_MK846_RC_AB01.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L59_MK846_DD_AB107/2020-03-16-200218L59_MK846_DD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L59_MK846_DD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L60_MK846_DC_AB107/2020-03-16-200218L60_MK846_DC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L60_MK846_DC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L61_MK846_RD_AB107/2020-03-16-200218L61_MK846_RD_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L61_MK846_RD_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200218L62_MK846_RC_AB107/2020-03-16-200218L62_MK846_RC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.protein_coding.merged.2020-03-16-200218L62_MK846_RC_AB107.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L81_exp200118_MS207_RAPA100_input/2020-03-16-200224L81_exp200118_MS207_RAPA100_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.protein_coding.merged.2020-03-16-200224L81_exp200118_MS207_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L82_exp200118_MS249_RAPA100_input/2020-03-16-200224L82_exp200118_MS249_RAPA100_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.protein_coding.merged.2020-03-16-200224L82_exp200118_MS249_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L83_exp200118_MS250_RAPA100_input/2020-03-16-200224L83_exp200118_MS250_RAPA100_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.protein_coding.merged.2020-03-16-200224L83_exp200118_MS250_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L84_exp200118_MS297_RAPA040_input/2020-03-16-200224L84_exp200118_MS297_RAPA040_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.protein_coding.merged.2020-03-16-200224L84_exp200118_MS297_RAPA040_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L85_exp200118_MS297_RAPA100_input/2020-03-16-200224L85_exp200118_MS297_RAPA100_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.protein_coding.merged.2020-03-16-200224L85_exp200118_MS297_RAPA100_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes.protein_coding.merged.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2020-03-16-200224L86_exp200118_MS297_RAPAON_input/2020-03-16-200224L86_exp200118_MS297_RAPAON_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.protein_coding.merged.2020-03-16-200224L86_exp200118_MS297_RAPAON_input.S_pombe-spike-in.a.RPKM -excludeReadsMappingToOtherChromosomes -fullFragmentMidPoint