python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L01_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L02_MS550_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L03_MS551_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L04_MS551_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L05_MS551_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L06_MS1_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L07_MS554_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L08_MS555_FrA_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L09_MS555_FrB_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L10_MS555_FrC_AB107.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L11_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L12_MS550_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_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.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_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.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_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.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_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.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_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.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_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.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_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.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_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.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_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.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_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.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_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.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_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.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L01_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L01_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L02_MS550_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L02_MS550_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L03_MS551_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L03_MS551_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L04_MS551_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L04_MS551_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L05_MS551_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L05_MS551_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L06_MS1_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L06_MS1_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L07_MS554_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L07_MS554_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L08_MS555_FrA_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L08_MS555_FrA_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L09_MS555_FrB_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L09_MS555_FrB_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L10_MS555_FrC_AB107.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L10_MS555_FrC_AB107.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L11_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L11_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L12_MS550_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L12_MS550_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L23_MS297_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L24_MS297_RAPAON_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L43_MS207_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L44_MS249_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L45_MS250_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L46_MS297_RAPA040_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L47_MS297_RAPA100_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L48_MS297_RAPAON_AB01.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_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.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_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.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_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.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_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.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_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.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_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.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_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.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_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.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L23_MS297_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L23_MS297_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L24_MS297_RAPAON_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L24_MS297_RAPAON_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L43_MS207_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L43_MS207_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L44_MS249_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L44_MS249_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L45_MS250_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L45_MS250_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L46_MS297_RAPA040_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L46_MS297_RAPA040_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L47_MS297_RAPA100_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L47_MS297_RAPA100_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L48_MS297_RAPAON_AB01.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L48_MS297_RAPAON_AB01.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPM -RPM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L13_MS551_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L14_MS551_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L15_MS551_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L16_MS1_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L17_MS554_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L18_MS555_FrA_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L19_MS555_FrB_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L20_MS555_FrC_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L19_MS207_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L20_MS249_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L21_MS250_RAPA100_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L22_MS297_RAPA040_input.2x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.a.RPKM -excludeReadsMappingToOtherChromosomes 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-upstream500bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-upstream500bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes TSS-250bp-350bp.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPM -RPM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.genes_500bp_ext 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.nochrM.chrom.sizes genes_500bp_ext.sacCer3.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes_500bp_ext 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPM -RPM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_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.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_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.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_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.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_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.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_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.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_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.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_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.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_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.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_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.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_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.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_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.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_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.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.a.RPKM -excludeReadsMappingToOtherChromosomes &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-upstream500bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPM -RPM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L13_MS551_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L13_MS551_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L14_MS551_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L14_MS551_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L15_MS551_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L15_MS551_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L16_MS1_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L16_MS1_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L17_MS554_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L17_MS554_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L18_MS555_FrA_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L18_MS555_FrA_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L19_MS555_FrB_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L19_MS555_FrB_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-191218L20_MS555_FrC_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-191218L20_MS555_FrC_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L19_MS207_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L19_MS207_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L20_MS249_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L20_MS249_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L21_MS250_RAPA100_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L21_MS250_RAPA100_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.TSS-250bp-350bp.bed 0 2020-02-21-200201L22_MS297_RAPA040_input.1x36mers.sacCer3+Schizosaccharomyces_pombe.ASM294v2.20.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2020-02-21-200201L22_MS297_RAPA040_input.sacCer3+Schizosaccharomyces_pombe.unique.RPKM &