python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.TSS-250bp-350bp.bed 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.a.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.2x36mers.a.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.a.RPM -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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-250bp-350bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes TSS-upstream500bp.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes_500bp_ext.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes genes.sacCer3.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-250bp-350bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes TSS-upstream500bp.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes_500bp_ext.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.unique.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.genes 0 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L01_MS1_sp124_input/190115_L01_MS1_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L01_MS1_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L02_MS438_0nM_sp124_input/190115_L02_MS438_0nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L02_MS438_0nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L03_MS438_10nM_sp124_input/190115_L03_MS438_10nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L03_MS438_10nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L04_MS438_30nM_sp124_input/190115_L04_MS438_30nM_sp124_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L04_MS438_30nM_sp124_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L05_MS1_sp124_AB102/190115_L05_MS1_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L05_MS1_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L06_MS438_0nM_sp124_AB102/190115_L06_MS438_0nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L06_MS438_0nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L07_MS438_10nM_sp124_AB102/190115_L07_MS438_10nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L07_MS438_10nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L08_MS438_30nM_sp124_AB102/190115_L08_MS438_30nM_sp124_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L08_MS438_30nM_sp124_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L09_MS1_sp124_AB107/190115_L09_MS1_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L09_MS1_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L10_MS438_0nM_sp124_AB107/190115_L10_MS438_0nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L10_MS438_0nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L11_MS438_10nM_sp124_AB107/190115_L11_MS438_10nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L11_MS438_10nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L12_MS438_30nM_sp124_AB107/190115_L12_MS438_30nM_sp124_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L12_MS438_30nM_sp124_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L13_MS1_sp127_input/190115_L13_MS1_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L13_MS1_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L14_MS441_0nM_sp127_input/190115_L14_MS441_0nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L14_MS441_0nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L15_MS441_10nM_sp127_input/190115_L15_MS441_10nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L15_MS441_10nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L16_MS441_30nM_sp127_input/190115_L16_MS441_30nM_sp127_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L16_MS441_30nM_sp127_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP/190115_L17_MS1_sp127_anti-v5_ChIP.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L17_MS1_sp127_anti-v5_ChIP.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L18_MS441_0nM_sp127_AB102/190115_L18_MS441_0nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L18_MS441_0nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L19_MS441_10nM_sp127_AB102/190115_L19_MS441_10nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L19_MS441_10nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L20_MS441_30nM_sp127_AB102/190115_L20_MS441_30nM_sp127_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L20_MS441_30nM_sp127_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L21_MS1_sp127_AB107/190115_L21_MS1_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L21_MS1_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L22_MS441_0nM_sp127_AB107/190115_L22_MS441_0nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L22_MS441_0nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L23_MS441_10nM_sp127_AB107/190115_L23_MS441_10nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L23_MS441_10nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190115_L24_MS441_30nM_sp127_AB107/190115_L24_MS441_30nM_sp127_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190115_L24_MS441_30nM_sp127_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L01_MS1_sp111_input/190121_L01_MS1_sp111_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L01_MS1_sp111_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L02_MS432_0nM_input/190121_L02_MS432_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L02_MS432_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L03_MS432_10nM_input/190121_L03_MS432_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L03_MS432_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L04_MS432_30nM_input/190121_L04_MS432_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L04_MS432_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L05_MS1_sp115_input/190121_L05_MS1_sp115_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L05_MS1_sp115_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L06_MS436_0nM_input/190121_L06_MS436_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L06_MS436_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L07_MS436_10nM_input/190121_L07_MS436_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L07_MS436_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L08_MS436_30nM_input/190121_L08_MS436_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L08_MS436_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L09_MS1A_sp112_input/190121_L09_MS1A_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L09_MS1A_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L10_MS430_0nM_input/190121_L10_MS430_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L10_MS430_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L11_MS430_10nM_input/190121_L11_MS430_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L11_MS430_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L12_MS430_30nM_input/190121_L12_MS430_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L12_MS430_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L13_MS1B_sp112_input/190121_L13_MS1B_sp112_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L13_MS1B_sp112_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L14_MS433_0nM_input/190121_L14_MS433_0nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L14_MS433_0nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L15_MS433_10nM_input/190121_L15_MS433_10nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L15_MS433_10nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L16_MS433_30nM_input/190121_L16_MS433_30nM_input.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L16_MS433_30nM_input.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L17_MS1_sp111_AB107/190121_L17_MS1_sp111_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L17_MS1_sp111_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L18_MS432_0nM_AB107/190121_L18_MS432_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L18_MS432_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L19_MS432_10nM_AB107/190121_L19_MS432_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L19_MS432_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L20_MS432_30nM_AB107/190121_L20_MS432_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L20_MS432_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L21_MS1_sp115_AB107/190121_L21_MS1_sp115_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L21_MS1_sp115_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L22_MS436_0nM_AB107/190121_L22_MS436_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L22_MS436_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L23_MS436_10nM_AB107/190121_L23_MS436_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L23_MS436_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L24_MS436_30nM_AB107/190121_L24_MS436_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L24_MS436_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L25_MS1A_sp112_AB107/190121_L25_MS1A_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L25_MS1A_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L26_MS430_0nM_AB107/190121_L26_MS430_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L26_MS430_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L27_MS430_10nM_AB107/190121_L27_MS430_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L27_MS430_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L28_MS430_30nM_AB107/190121_L28_MS430_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L28_MS430_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L29_MS1B_sp112_AB107/190121_L29_MS1B_sp112_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L29_MS1B_sp112_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L30_MS433_0nM_AB107/190121_L30_MS433_0nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L30_MS433_0nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L31_MS433_10nM_AB107/190121_L31_MS433_10nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L31_MS433_10nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L32_MS433_30nM_AB107/190121_L32_MS433_30nM_AB107.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L32_MS433_30nM_AB107.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L33_MS1_sp111_AB102/190121_L33_MS1_sp111_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L33_MS1_sp111_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L34_MS432_0nM_AB102/190121_L34_MS432_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L34_MS432_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L35_MS432_10nM_AB102/190121_L35_MS432_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L35_MS432_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L36_MS432_30nM_AB102/190121_L36_MS432_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L36_MS432_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L37_MS1_sp115_AB102/190121_L37_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L37_MS1_sp115_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L38_MS436_0nM_AB102/190121_L38_MS436_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L38_MS436_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L39_MS436_10nM_AB102/190121_L39_MS436_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L39_MS436_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L40_MS436_30nM_AB102/190121_L40_MS436_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L40_MS436_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L41_MS1A_sp112_AB102/190121_L41_MS1A_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L41_MS1A_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L42_MS430_0nM_AB102/190121_L42_MS430_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L42_MS430_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L43_MS430_10nM_AB102/190121_L43_MS430_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L43_MS430_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L44_MS430_30nM_AB102/190121_L44_MS430_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L44_MS430_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L45_MS1B_sp112_AB102/190121_L45_MS1B_sp112_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L45_MS1B_sp112_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L46_MS433_0nM_AB102/190121_L46_MS433_0nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L46_MS433_0nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L47_MS433_10nM_AB102/190121_L47_MS433_10nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L47_MS433_10nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L48_MS433_30nM_AB102/190121_L48_MS433_30nM_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L48_MS433_30nM_AB102.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 /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/datasets-ChIP/2019-02-15-190121_L49_MS1_sp115_AB102/190121_L49_MS1_sp115_AB102.1x36mers.unique.nochrM.bam /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.nochrM.chrom.sizes genes.S_pombe.2019-02-15-190121_L49_MS1_sp115_AB102.unique.RPM -RPM